Next generation Glucose-1-phosphate thymidylyltransferase (RmlA) inhibitors: An extended SAR study to direct future design

Ganyuan Xiao,Magnus S Alphey,Fanny Tran,Lisa Pirrie,Pierre Milbeo,Yi Zhou,Jasmine K Bickel,Oxana Kempf,Karl Kempf,James H Naismith,Nicholas J Westwood

doi:10.1016/j.bmc.2021.116477

Ganyuan Xiao, Magnus S Alphey + Show 9 more

Open Access

https://doi.org/10.1016/j.bmc.2021.116477

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Abstract

The monosaccharide l-Rhamnose is an important component of bacterial cell walls. The first step in the l-rhamnose biosynthetic pathway is catalysed by glucose-1-phosphate thymidylyltransferase (RmlA), which condenses glucose-1-phosphate (Glu-1-P) with deoxythymidine triphosphate (dTTP) to yield dTDP-d-glucose. In addition to the active site where catalysis of this reaction occurs, RmlA has an allosteric site that is important for its function. Building on previous reports, SAR studies have explored further the allosteric site, leading to the identification of very potent P. aeruginosa RmlA inhibitors. Modification at the C6-NH2 of the inhibitor’s pyrimidinedione core structure was tolerated. X-ray crystallographic analysis of the complexes of P. aeruginosa RmlA with the novel analogues revealed that C6-aminoalkyl substituents can be used to position a modifiable amine just outside the allosteric pocket. This opens up the possibility of linking a siderophore to this class of inhibitor with the goal of enhancing bacterial cell wall permeability.

Highlights

The continued global emergence of multi-drug resistant bacteria is a major health concern
The L-rhamnose biosynthetic pathway involves four enzymes, RmlA-RmlD, which catalyse the conversion of glucose-1-phosphate (Glu-1-P) to the L-rhamnose precursor deoxythymidine diphosphate-Lrhamnose
No attempts to optimize the substituent at the N1-position were made. This current study started with examination of the reported structure of the RmlA-8a complex [PDB 4ASJ] and revealed that the N1-substituent pocket was formed from both main- and sidechain atoms of residues Leu[45], His[119], Glu[120], Ile[256], Arg[259] and Gln[260] (Figure 1B)

Summary

Introduction

The continued global emergence of multi-drug resistant bacteria is a major health concern. The development of novel antimicrobials that avoid the existing mechanisms of resistance and target new path ways is recognised as a high priority for research. The enzymes involved in the biosynthesis of L-rhamnose are potential anti-tuberculosis drug targets.[5,6] The L-rhamnose biosynthetic pathway involves four enzymes, RmlA-RmlD, which catalyse the conversion of glucose-1-phosphate (Glu-1-P) to the L-rhamnose precursor deoxythymidine diphosphate-Lrhamnose (dTDP-L-rhamnose[3], Scheme 1). Since this biosynthetic pathway is not found in eukaryotes, these enzymes are attractive targets for the development of novel selective antibiotics. Small molecule in hibitors of RmlA7–9 and RmlC10–11 have already been reported

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